SMTL ID : 5cnv.1

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to GDP and TTP at 3.20 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-4-4-mer

Ligands

4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 21 residues within 4Å: Chain A: P.208, T.209, S.224, C.225, A.252, G.253, R.298, G.299, G.300, A.301, N.437, L.438, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.209, A:A.252, A:G.253, A:R.298, A:G.299, A:A.301, A:N.437, A:E.441, A:S.622, A:E.623, A:T.624, A:S.625, A:S.625, A:S.625, A:S.625 Salt bridges: A:R.298 pi-Cation interactions: A:R.298, A:R.298 GDP.7: 21 residues within 4Å: Chain B: P.208, T.209, S.224, C.225, A.252, G.253, R.298, G.299, G.300, A.301, N.437, L.438, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.209, B:T.209, B:T.209, B:T.209, B:A.252, B:G.253, B:R.298, B:G.299, B:A.301, B:N.437, B:E.441, B:S.622, B:E.623, B:T.624, B:S.625 Salt bridges: B:R.298 pi-Cation interactions: B:R.298, B:R.298 GDP.13: 20 residues within 4Å: Chain C: P.208, T.209, S.224, C.225, A.252, G.253, R.298, G.299, A.301, N.437, L.438, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:T.209, C:T.209, C:A.252, C:G.299, C:A.301, C:N.437, C:E.441, C:S.622, C:E.623, C:T.624, C:S.625, C:S.625 Water bridges: C:L.438, C:L.438 Salt bridges: C:R.298 pi-Cation interactions: C:R.298, C:R.298 GDP.19: 21 residues within 4Å: Chain D: P.208, T.209, S.224, C.225, A.252, G.253, R.298, G.299, G.300, A.301, N.437, L.438, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:T.209, D:T.209, D:T.209, D:A.252, D:G.253, D:R.298, D:G.299, D:A.301, D:E.441, D:S.622, D:E.623, D:T.624, D:T.624, D:S.625 Water bridges: D:V.226, D:L.438 Salt bridges: D:R.298 pi-Cation interactions: D:R.298, D:R.298

4 x DAT: 2'-DEOXYADENOSINE-5'-DIPHOSPHATE(Non-covalent)

DAT.2: 18 residues within 4Å: Chain A: V.7, K.9, R.10, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, I.58, H.59, I.62, F.87, K.91 Ligands: MG.3, TTP.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.25 Hydrogen bonds: A:R.10, A:E.15, A:E.15, A:N.18, A:T.55, A:H.59 Water bridges: A:K.91, A:K.91 Salt bridges: A:K.9, A:R.10, A:K.91, A:K.91 DAT.8: 18 residues within 4Å: Chain B: V.7, K.9, R.10, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, I.58, H.59, I.62, F.87, K.91 Ligands: MG.9, TTP.10 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.25 Hydrogen bonds: B:R.10, B:E.15, B:N.18, B:T.55, B:H.59 Water bridges: B:K.91, B:K.91 Salt bridges: B:K.9, B:R.10, B:K.91, B:K.91 DAT.14: 18 residues within 4Å: Chain C: V.7, K.9, R.10, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, I.58, H.59, I.62, F.87, K.91 Ligands: MG.15, TTP.16 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.25 Hydrogen bonds: C:R.10, C:E.15, C:E.15, C:N.18, C:T.55, C:H.59 Water bridges: C:K.91, C:K.91 Salt bridges: C:K.9, C:R.10, C:K.91, C:K.91 DAT.20: 16 residues within 4Å: Chain D: V.7, K.9, R.10, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, H.59, F.87, K.91 Ligands: MG.21, TTP.22 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.25 Hydrogen bonds: D:R.10, D:E.15, D:N.18, D:H.59 Water bridges: D:K.91, D:K.91 Salt bridges: D:K.9, D:R.10, D:K.91, D:K.91

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain A: K.91 Ligands: DAT.2, TTP.4 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: TTP.5 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Ligands: DAT.8, TTP.10 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: TTP.11 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Ligands: DAT.14, TTP.16 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Ligands: TTP.17 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Ligands: DAT.20, TTP.22 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Ligands: TTP.23 No protein-ligand interaction detected (PLIP)

8 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.4: 9 residues within 4Å: Chain A: K.9, K.21, R.24, V.25, W.28, K.91, F.97 Ligands: DAT.2, MG.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.97 Hydrogen bonds: A:R.24, A:R.24 Water bridges: A:K.91 Salt bridges: A:K.9, A:K.9, A:K.21, A:K.21, A:K.91 pi-Stacking: A:W.28 TTP.5: 12 residues within 4Å: Chain A: D.232, S.233, L.234, I.261, R.262, I.268, R.269, H.275, F.281 Chain B: S.249, C.292 Ligands: MG.6 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.234, A:L.234, A:I.268, A:F.281 Hydrogen bonds: A:D.232, A:L.234, A:R.269, B:C.292 Water bridges: A:R.262, A:R.262, A:G.270, A:G.270 Salt bridges: A:R.262, A:R.269 TTP.10: 8 residues within 4Å: Chain B: K.9, K.21, R.24, V.25, W.28, F.97 Ligands: DAT.8, MG.9 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.28, B:W.28, B:F.97 Hydrogen bonds: B:R.24, B:R.24 Water bridges: B:K.91 Salt bridges: B:K.9, B:K.9, B:K.21, B:K.21, B:R.24, B:K.91 pi-Stacking: B:W.28 TTP.11: 12 residues within 4Å: Chain A: S.249, C.292 Chain B: D.232, S.233, L.234, I.261, R.262, I.268, R.269, H.275, F.281 Ligands: MG.12 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.234, B:I.268, B:F.281 Hydrogen bonds: B:D.232, B:L.234, B:R.269, A:C.292 Water bridges: B:R.262, B:R.262 Salt bridges: B:R.262, B:R.269 TTP.16: 9 residues within 4Å: Chain C: K.9, K.21, R.24, V.25, W.28, K.91, F.97 Ligands: DAT.14, MG.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.97 Hydrogen bonds: C:R.24, C:R.24 Water bridges: C:K.91, C:K.91 Salt bridges: C:K.9, C:K.9, C:K.21, C:K.21, C:R.24, C:K.91 TTP.17: 12 residues within 4Å: Chain C: D.232, S.233, L.234, I.261, R.262, I.268, R.269, H.275, F.281 Chain D: S.249, C.292 Ligands: MG.18 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.234, C:L.234, C:I.268, C:F.281 Hydrogen bonds: C:D.232, C:L.234, C:R.269, D:C.292 Water bridges: C:R.262, C:R.262 Salt bridges: C:R.262, C:R.269 TTP.22: 8 residues within 4Å: Chain D: K.9, K.21, R.24, V.25, W.28, F.97 Ligands: DAT.20, MG.21 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.28, D:F.97 Hydrogen bonds: D:E.15, D:R.24, D:R.24 Water bridges: D:K.91 Salt bridges: D:K.9, D:K.9, D:K.21, D:K.21, D:K.91 pi-Stacking: D:W.28 TTP.23: 12 residues within 4Å: Chain C: S.249, C.292 Chain D: D.232, S.233, L.234, I.261, R.262, I.268, R.269, H.275, F.281 Ligands: MG.24 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.234, D:L.234, D:I.268, D:F.281 Hydrogen bonds: D:D.232, D:L.234, D:R.269, C:C.292 Water bridges: D:R.262 Salt bridges: D:R.262, D:R.269

4 x FEO: MU-OXO-DIIRON(Non-covalent)

FEO.25: 6 residues within 4Å: Chain E: D.84, E.115, H.118, E.204, E.238, H.241 8 PLIP interactions: 7 interactions with chain E, 1 Ligand-Water interactions, Metal complexes: E:D.84, E:E.115, E:E.115, E:H.118, E:E.204, E:E.238, E:E.238, H2O.2 FEO.26: 6 residues within 4Å: Chain F: D.84, E.115, H.118, E.204, E.238, H.241 9 PLIP interactions: 7 interactions with chain F, 2 Ligand-Water interactions, Water bridges: F:Q.87 Metal complexes: F:D.84, F:E.115, F:E.115, F:H.118, F:E.204, F:H.241, H2O.2, H2O.2 FEO.27: 6 residues within 4Å: Chain G: D.84, E.115, H.118, E.204, E.238, H.241 8 PLIP interactions: 7 interactions with chain G, 1 Ligand-Water interactions, Metal complexes: G:D.84, G:E.115, G:H.118, G:E.204, G:E.238, G:E.238, G:H.241, H2O.2 FEO.28: 6 residues within 4Å: Chain H: D.84, E.115, H.118, E.204, E.238, H.241 8 PLIP interactions: 6 interactions with chain H, 2 Ligand-Water interactions, Metal complexes: H:D.84, H:E.115, H:H.118, H:E.238, H:E.238, H:H.241, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimanyi, C.M. et al., Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli. Elife (2016)

Release Date

2016-01-20

Peptides

Ribonucleoside-diphosphate reductase 1 subunit alpha: ABCD
Ribonucleoside-diphosphate reductase 1 subunit beta: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Ribonucleoside-diphosphate reductase 1 subunit alpha

Ribonucleoside-diphosphate reductase 1 subunit beta

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